GRangesMapping-class {GenomicRanges} | R Documentation |
The GRangesMapping class is a container for both the genomic
locations and the matching results output from the map
function.
The map
generic converts a set of ranges to the equivalent
ranges on another sequence, through some sort of alignment between
sequences, and outputs a GRangesMapping
object. There are two
components of that object: the transformed GRanges, and the
hits
, a Hits
object of the same length
that matches each input range to a destination sequence (useful when
the alignment is one/many to many).
GRangesMapping
Accessorsgranges(x)
: Gets the mapped GRanges.
hits(x)
: Gets the matching between the input ranges
and the destination sequences (of which there may be more than
one).
dim(x)
: Same as dim(hits(x))
.
length(x)
: Same as length(hits(x))
.
subjectHits(x)
: Same as subjectHits(hits(x))
.
queryHits(x)
: Same as queryHits(hits(x))
.
GRangesMapping
Coercionas(from, "RangedData")
: Converts
a GRangesMapping
into
a RangedData
. The ranges
/space
in the RangedData
are the ranges
/space
of from
, and the values
result from the coercion of
the hits
to a DataFrame
.
as(from, "GenomicRanges")
: Returns the
GRanges
with the hits
(coerced to a DataFrame
) as the mcols
.
Michael Lawrence
Methods on the generic map
, which generates an instance of
this class, are defined in other packages, like GenomicRanges.
# See ?map-methods in GenomicRanges or GenomicAlignments for examples.